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Genes 2018, 9(8), 409; https://doi.org/10.3390/genes9080409

Using the Mutation-Selection Framework to Characterize Selection on Protein Sequences

1
Department of Integrative Biology, Institute for Cellular and Molecular Biology, and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA
2
Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA 19122, USA
*
Author to whom correspondence should be addressed.
Received: 19 June 2018 / Revised: 2 August 2018 / Accepted: 9 August 2018 / Published: 13 August 2018
(This article belongs to the Special Issue Evolution and Structure of Proteins and Proteomes)
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Abstract

When mutational pressure is weak, the generative process of protein evolution involves explicit probabilities of mutations of different types coupled to their conditional probabilities of fixation dependent on selection. Establishing this mechanistic modeling framework for the detection of selection has been a goal in the field of molecular evolution. Building on a mathematical framework proposed more than a decade ago, numerous methods have been introduced in an attempt to detect and measure selection on protein sequences. In this review, we discuss the structure of the original model, subsequent advances, and the series of assumptions that these models operate under. View Full-Text
Keywords: evolutionary modeling; protein evolution; mutation-selection models evolutionary modeling; protein evolution; mutation-selection models
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).
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Teufel, A.I.; Ritchie, A.M.; Wilke, C.O.; Liberles, D.A. Using the Mutation-Selection Framework to Characterize Selection on Protein Sequences. Genes 2018, 9, 409.

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